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WORLD INTELLECTUAL PROPERTY ORGANIZATION
International Bureau

PCT

INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT)

(51) International Patent Classification 6 :

G01N 33/53, 33/574, A01N 37/18, A61K
38/00

(11) International Publication Number: WO 97/34146

(43) International Publication Date: 18 September 1997 (18.09.97)

(21) International Application Number: PCT/US97/0388 1

(22) International Filing Date: 12 March 1997 (12.03.97)

(30) Priority Data:

60/013,274
08/814,836

12 March 1996 (12.03.96) US
1 1 March 1997 (1 1 .03.97) US

(71) Applicants: THE GENERAL HOSPITAL CORPORATION

[US/US]; 55 Fruit Street, Boston, MA 02114 (US). INDI-
ANA UNIVERSITY FOUNDATION [US/US]; 1120 West
South Drive, Indianapolis, IN 46202-5113 (US).

(72) Inventors: AVRUCH, Joseph; 277 St. Paul Street, Brookline,

MA 02146 (US). LUO, Zhujun; 235 Deny Road, Chestnut
Hill, MA 02167 (US). MARSHAIL, Mark, S.; 1519 Spruce
Court, Carmel, IN 46033 (US).

(74) Agent: FRASER, Janis, K.; Fish & Richardson P.C., 225
Franklin Street, Boston, MA 02110 (US).

(81) Designated States: CA, JP, European patent (AT, BE, CH, DE,
DK, ES, FI, FR, GB, GR, IE, IT, LU. MC, NL, PT, SE).

Published

With international search report.

Before the expiration of the time limit for amending the
claims and to be republished in the event of the receipt of
amendments.

(54) Title: INHIBITING PROTEIN INTERACTIONS
(57) Abstract

The invention discloses methods of inhibiting direct binding of Ras with Raf and screening methods to identify compounds which
inhibit direct binding of Ras to Raf, Raf activation, and cell proliferation.

FOR THE PURPOSES OF INFORMATION ONLY

Codes used to identify States party to the PCT on the front pages of pamphlets publishing international
applications under the PCT.

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United States of America

Uzbekistan

Viet Nam

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INHIBTTTNG PROTEIN IN TERACTIONS
Cross Reference to Related Ap plications
This application claims priority from provisional
5 application 60/013,271, filed on March 12, 1996.

Statement as to Federally Spon sored Research
This invention was made with Government support
under DK41513 and DK41762 awarded by the National
Institutes of Diabetes and Digestive and Kidney Diseases.
10 The Government has certain rights in the invention.

Background of the Invention
The invention relates to signal transduction.
The ras gene was discovered as an oncogene of the
Harvey (rasH) and Kirsten (rasK) rat sarcoma viruses.
15 In humans, characteristic mutations in the cellular ras
gene (c-ras) have been associated with many different
types of cancers. These mutant alleles, which render Ras
const itutively active, have been shown to transform
cells, such as the murine cell line NIH 3T3, in culture.
0 The ras gene product binds to guanine triphosphate

(GTP) and guanine diphosphate (GDP) and hydrolyzes GTP to
GDP. It is the GTP-bound state of Ras (Ras -GTP) that is
active. An accessory molecule, GTPase-activating
protein (GAP) also binds to Ras and accelerates the
5 hydrolysis of GTP. The ras proto-oncogene requires a
functionally intact raf-l proto-oncogene in order to
transduce growth and differentiation signals initiated by
receptor and non-receptor tyrosine kinases in higher
eukaryotes. Activated Ras is necessary for the
0 activation of the c-raf-1 proto-oncogene, but the

biochemical steps through which Ras activates the Raf-l
protein (Ser/Thr) kinase are not well characterized.

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Summary of the Invention
It has now been discovered that Raf binds to Ras-
GTP through two relatively independent interactions. Raf
amino acids 50-150 (SEQ ID NO: 5) bind to the Ras effector
5 loop (Ras residues 32-40; SEQ ID NO: 3) and the Raf zinc
finger domain binds to an epitope present only in
prenylated Ras. These interactions participate in the
transduction of an intracellular signal via the Ras-Raf
mediated signal transduction pathway which culminates in
10 cell proliferation.

Accordingly, the invention features a method of
reducing proliferation of cells in a mammal which
includes the steps of administering to the mammal, or
contacting the cells with, a compound which inhibits
15 direct binding of a non-effector loop domain of Ras,
e.g., a portion of Ras which is distinct from the
effector loop domain and contains a prenylated epitope,
with a zinc finger domain of Raf. Preferably, the mammal
is a human and the compound reduces Raf enzymatic

2 0 activity, e.g., Raf kinase activity. The compound may be

a zinc finger domain-containing polypeptide, such as a
polypeptide containing the consensus amino acid sequence
of HXXXXXXXXXXXXCXXCXXXXXXXXXCXXCXXXXHXXCXXXXXXXC (SEQ ID
NO;l) where X can be any amino acid, e.g., a polypeptide
25 containing the zinc finger domain of Raf, amino
acids 139-184 of Raf

(HNFARKTFLKLAFCDICQKFLLNGFRCQTCGYKFHEHCSTKVPTMC; SEQ ID
NO:2). In another embodiment, the compound includes a
lipid moiety which binds to a zinc finger domain of Raf.

3 0 Preferably, the lipid moiety is a farnesyl moiety For

example, the compound may contain a carboxy terminal
fragment of Ras which contains a carboxyterminal farnesyl
moiety at position C 186 .

The method may also include the step of
35 administering to the mammal or contacting the cells with

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a second, different compound which inhibits direct
binding of the effector loop domain of Ras with an amino-
terminal Ras-binding domain of Raf. For example, the
compound may be a polypeptide containing the effector
5 loop domain of Ras, e.g., amino acids 32-40 of Ras
(YDPTIEDSY; SEQ ID NO: 3). In other embodiments, the
compound may be a polypeptide containing amino acids 84-
87 of Raf (KALK; SEQ ID NO: 4) or a polypeptide containing
amino acids 50-150 of Raf
1 0 ( DPSKTSNTIRVFLPNKQRTVVNVRNGMSLHDCLMKALKVRGLQPECCAVFRIiLHEH
KGKKARLDWNTDAASLI GEELQVDFLDHVPLTTHNFARKTFLKLA ; SEQ ID
NO: 5) .

The invention also features a method of screening
candidate compounds to identify a compound capable of

15 inhibiting direct binding of Ras to Raf which includes
the steps of (a) providing a zinc finger domain-
containing fragment of Raf; (b) providing a Raf-binding
fragment of Ras; (c) contacting the zinc finger domain-
containing fragment of Raf or the Raf-binding fragment of

2 0 Ras with a candidate compound; and (d) determining the
binding of the zinc finger domain-containing fragment of
Raf and the Raf-binding fragment of Ras. The Raf
fragment may first be contacted with the compound,
followed by contact with the Ras fragment and subsequent

25 measurement of Ras-Raf binding. Alternatively, the Ras
fragment may first be contacted with the compound,
followed by contact with the Raf fragment and subsequent
measurement of Ras-Raf binding. In another variation of
the assay, the Ras fragment, Raf fragment and the

30 candidate compound may all be incubated together
simultaneously, followed by measurement of Ras-Raf
binding. In another variation, Ras and Raf may be
allowed to bind and then contacted with the compound,
after which Ras-Raf binding is measured. In this manner,

35 the ability of the compound to disrupt pre-bound Ras-Raf
may be evaluated. In vitro and/or in situ Ras-Raf

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binding may be measured using a variety of methods known
in the art, such as coimmunoprecipitation . A decrease in
binding in the presence of the compound compared to that
in the absence of the compound indicates that the
5 compound inhibits direct binding of Ras to Raf .

Preferably, the zinc finger domain-containing fragment of
Raf comprises the amino acid sequence of SEQ ID NO: 1;
more preferably, the Raf fragment includes the amino acid
sequence of SEQ ID NO: 2. The Raf -binding fragment of Ras
10 is preferably post-translationally modified to add a

lipid moiety such as a farnesyl moiety, e.g., a farnesyl
moiety located at position C 186 of eukaryotic prenylated
Ras .

The invention also includes a method of screening
15 candidate compounds to identify a compound capable of

inhibiting Raf activation which includes the steps of (a)
providing a fragment of Raf comprising a zinc finger
domain, e.g., a CRl domain containing an intact zinc
finger domain, and a kinase catalytic domain, e.g, the
20 CR3 domain of Raf; (b) providing a Raf-binding fragment
of Ras, e.g, a GTP-bound prenylated fragment of Ras; (c)
contacting the fragment of Raf or Raf-binding fragment of
Ras with a candidate compound; and (d) determining the
Raf kinase activity of the Raf fragment. A decrease in
25 activity in the presence of the compound compared to that
in the absence of the compound indicates that the
compound inhibits Raf activation.

Also within the invention is a method of screening
candidate compounds to identify a compound capable of
30 inhibiting cell proliferation, e.g., proliferation

associated with transformed cells, i.e., cancer cells,
which includes the steps of (a) providing a cell
transfected with a substantially pure DNA encoding a
transformation-competent Ras such as Ha-Ras (V12 ) , Ras
35 CaaX, or myristoylated Ras; (b) contacting the cell with

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a candidate compound; and (c) determining the amount of
proliferation of the cell. For example, the cell may be
a fibroblast cell, and cell proliferation may be
evaluated by measuring foci formation of the cells, an
5 indication of cell transformation. A decrease in cell
proliferation in the presence of the candidate compound
compared to that in the absence of the candidate compound
indicates that the candidate compound inhibits cell
proliferation, e.g, unwanted proliferation such as that

10 associated with cancerous, i.e., transformed cells.

"Substantially pure" as used herein refers to a
DNA which has been purified from the sequences which
flank it in a naturally occurring state, i.e., a DNA
fragment which has been removed from the sequences which

15 are normally adjacent to the fragment, e.g., the

sequences adjacent to the fragment in the genome in which
it naturally occurs, and which has been substantially
purified from other components which naturally accompany
the DNA, e.g., DNA which has been purified from the

20 proteins which naturally accompany it in the cell.

Other features and advantages of the invention
will be apparent from the following detailed description
and from the claims.

Detailed Description

25 The drawings will first be briefly described.

Drawings

Fig. 1A is a diagram showing the structure of
c-Raf-l and chimeric protein kinase C (PKC)Y/Raf with
conserved domains CR1, CR2 , and CR3 . CR1 encompasses
30 most of the Ras binding domain (amino acids 50-150; SEQ
ID NO: 5) which binds to the effector loop domain of Ras
and overlaps with the cysteine-rich region, Raf amino
acids 139-184 (SEQ ID NO:2). CR2 is Ser-Thr rich, and
CR3 encompasses the kinase catalytic domain.

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Fig. IB is a diagram showing an alignment of the
zinc finger domains of c-Raf-1 and PKC Y - The conserved
Cys and His residues in the two zinc fingers have been
aligned and are shown in bold type. The amino acid
5 sequence of the chimeric y/Raf protein is indicated: to
construct chimeric Y/Raf > DNA sequences encoding Raf
amino acids 150-177 (AFCDICQKFLLNGFRCQTCGYKFHEHCS; SEQ ID
NO: 6) were deleted, and replaced with the zinc finger
domain of PKCy (amino acids 99-152 of PKCy;
1 0 RNKHKFRLHS YSSPTFCDHCGSLLYGLVHQGGMKCSCCEMNVHRRCVRS VPSLCG ;

SEQ ID NO : 7 ) .

Fig. 2A is a bar graph showing activation of
wildtype and zinc finger variants of Raf by epidermal
growth factor (EGF) and phorbol myristate acetate (PMA) .
15 COS M7 cells were transfected with 5 fig of cDNA encoding
Myc-tagged versions of wildtype c-Raf-1 (lanes 1-3), Raf
(C165, 168S) (lanes 4-6), Y/Raf chimera (lanes 7-9), and
a Y/Raf chimera with inactivating mutations in the y zinc
finger (lanes 10-12). Thirty hours after transf ection,
20 cells were deprived of serum for 16 hours, followed by
the addition of EGF (50 ng/ml; lanes 2, 5, 18, 11) and
PMA (1 MM; lanes 3, 6, 9 and 12) or carrier (control;
lanes 1, 4, 7, 10). The cells were extracted 15 minutes.
The recombinant Raf polypeptides were immunoprecipitated
25 by anti-Myc monoclonal antibody 9B7.3. The kinase assay
was performed by sequential incubation of the immune
complex retained on protein G-sepharose beads with
GST-MEK1 and Erk-l. The 32 P-labeled polypeptides were
resolved on SDS-PAGE, transferred to PVDF membrane and
3 0 visualized by autoradiography using anti-Myc monoclonal
antibody 9E10.2. The 32 P-Erk-l was measured by liquid
scintillation counting of the excised band.

Fig. 2B is an autoradiograph showing incorporation

of 32 P into MEK-l and Erk-l.
35 Fig.2Cisa photograph of an immunoblot.

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Fig. 2D is a bar graph showing PMA activation of
Y/Raf. COS cells expressing Myc-Raf (solid bars) or
Y/Raf (open bars) were treated with PMA (1 /iM) for 1 or
24 hours; the latter cells were then restimulated with
5 PMA or EGF for an additional 15 minutes.

Fig 3A is a bar graph showing the importance of
Raf binding to the Ras effector loop in the activation of
wildtype Raf and y/Ra.f. cDNAs were transfected into COS
M7 cells: wildtype Raf (lanes 1-3; Raf (84-87A) (lanes
10 4-6); Y/Raf (lanes 7-9); and Y/Raf (84-87A) (lanes
10-12) . Cells deprived of serum for 18 hrs were
stimulated by treatment with EGF, 50 ng/ml (lanes 2, 5,
8, 11), PMA, 1 fM (lanes 3, 6, 9, 12) or carrier
(control; lanes 1, 4, 7, 10) for 15 min. prior to
15 extraction.

Fig. 3B is an autoradiograph showing incorporation
of 32 P into MEK-1 and Erk-1.

Fig. 3C is a photograph of an immunoblot.

Fig. 4A is a photograph of an anti-Myc immunoblot

2 0 (9E10.2) of Myc-Raf variants in the COS cell extracts.

Fig. 4B is a photograph of an anti-FLAG-Ras
immunoblot of the anti-FLAG antibody M2 immunoprecipitate
recovered on protein G sepharose.

Fig. 4C is a photograph of an anti-Myc immunoblot
25 (9E10.2) of the anti-FLAG M2 immunoprecipitate. For the
experiments shown in Figs. 4A-4C, each of the cDNAs
encoding the Myc-Raf variants (5 /xg) was cotransf ected
with FLAG —Ha -Ra s (V12) (5 nq) into COS cells. Cells were
extracted 4 8 hours after transf ection . The recombinant
30 FLAG— Ras was purified using anti-FLAG monoclonal antibody
M2 and protein G sepharose. The immune complex was
resolved by SDS-PAGE and subjected to immunoblotting .

Fig 5A is an anti-Myc immunoblot (9E10.2) of cell
extracts (0.1 mg protein) prepared from cells transfected

3 5 with Myc-Raf variants.

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Fig. 5B is an anti-Myc immunoblot of the
polypeptide complex retained by immobilized COS
recombinant Ras (V12) . For Figs. 5A and 5B f the cDNA
encoding FLAG Ha-Ras (V12) was transfected into COS
5 cells. Cell extracts were prepared 48 hours thereafter,
and aliquots containing 2 mg protein were subjected to
immunoprecipitation with anti-FLAG monoclonal antibody
M2. After purification on protein G-sepharose, the
immobilized COS recombinant Ras was labeled with y-S-GTP

10 and incubated at 4°C for 1 hour with an aliquot of an
extract prepared from COS cells transfected 48 hours
previously with cDNA encoding the Myc Raf variants
indicated; each aliquot contained 1 mg total protein.
After three washes with lysis buffer, the polypeptide

15 complexes were subjected to SDS PAGE and immunob lotting .

Fig 6A is an anti-Myc immunoblot (9E10.2) of the
extracts (0.1 mg protein) prepared from cells transfected
with Myc-Raf variants.

Fig. 6B is an anti-Myc immunoblot of the
20 polypeptide complex retained by immobilized bacterial
GST-Ras / GTPyS . For Figs. 6A and 6B, prokaryotic
recombinant GST-Ha— Ras was labeled with y-S-GTP.
Aliquots containing 5 fxg protein were incubated with
aliquots of cell lysates (containing 1 mg protein) of COS
2 5 cells transiently expressing the Myc Raf variants. After
1 hr at 4°C, the complexes were adsorbed by glutathione
Sepharose 4B, washed thrice, subjected to SDS-PAGE and
immunoblotted with anti-Myc antibody (9E10.2) to detect
the Myc-Raf polypeptides that associate with GST Ras -GTP .
30 F ig. 7A is an immunoblot showing that binding of a

zinc finger domain-containing Raf fusion protein
(GST-Raf , 130-220) , containing amino acids 130-220 of Raf
(FLDHVPLTTHNFARKTFLKLAFCDICQKFLLNGFRCQTCGYKFHEHCSTKVPTMCV

DWSNIRQLLLFPNSTIGDSGVPALPSLTMRRMRES; SEQ ID NO: 18) to Ras

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is not GTP-dependent but rather dependent on Ras-
f arnesylation. In contrast, binding of a Raf fusion
protein containing the primary Ras binding site, GST— Raf ,
50-150 which contains amino acids 50-150 of Raf
5 ( DPSKTSNTIRVFLPNKQRTVVNVRNGMSLHDCLMKALiKVRGLQPECCAVFRIjIjHEH
KGKKARLDWNTDAASLIGEELQVDFLDHVPLTTHNFARKTFLKLA; SEQ ID
NO: 5) is GTP-dependent.

Fig. 7B is a photograph of an electrophoretic gel
in which the fusion proteins in Fig. 7A (GST Raf, 50-150
10 and GST Raf 13 0-22 0) were stained with Coomassie Blue.
Raf zinc finger domain has multiple functions in Raf
activation

Cell proliferation is the culmination of a
successfully transduced intracellular signal, e.g, an

15 intracellular signal transduced via the Ras— mediated
signal transduction pathway which can be improperly
turned on in many types of cancer. Inhibition of Ras-Raf
binding interrupts transduction of an intracellular
signal along the Ras signal transduction pathway, and

20 thus, inhibits cell proliferation. The data described
herein indicate that inhibition of the Ras-Raf
interaction using the compositions and methods of the
invention is a promising approach to treating cancer and
other diseases characterized by unwanted cell

25 proliferation.

The function of the c-Raf-1 zinc finger domain in
the activation of the Raf kinase was analyzed using zinc
finger structures which differ from the wild type Raf
zinc finger. Mutation of Raf Cys 165/168 to Ser was

30 found to strongly inhibit the Ras dependent activation of
c-Raf-l by EGF. Deletion of the Raf zinc finger and
replacement with a homologous zinc finger from PKCy
(y/Raf) also abrogated EGF- induced activation, but
enabled a vigorous PMA-induced activation, which occurs

3 5 through a Ras- independent mechanism. Although y/Raf

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binds PMA, activation of y/Raf by PMA in situ is
indirect, inasmuch as PMA addition in vitro does not
activate y/Raf. The impaired ability of Ras-GTP to
activate the Raf zinc finger variants in situ is
attributable to at least two factors related to Raf
function. One factor is a decrease in Ras binding; both
Raf zinc finger variants exhibited decreased association
with Ras (V12) in situ on coexpression in COS cells, as
well as diminished binding in vitro to immobilized COS
recombinant prenylated Ras (V12)-GTP. In contrast, Raf
binding to unprenylated prokaryotic recombinant Ras-GTP
is unaffected by Raf zinc finger mutation. The second
factor is a decrease in the activation of Raf catalytic
function as reflected by transforming activity. Zinc
15 finger mutation (C165, 168S) severely inhibited the
Ras- independent transforming activity of Raf CaaX, a
potent transforming agent, which is a Ras -independent
membrane -bound form of Raf.

The Raf zinc finger plays an important role in the
20 overall binding of Raf to Ras-GTP in situ, and once Raf
is recruited to the membrane, an intact zinc finger is
necessary for the transition to an active state, perhaps
through the binding of a membrane lipid. Zinc finger
domain-mediated binding of Raf to Ras leads to Raf

2 5 activation, a critical event in the cellular signal

transduction pathway which culminates in cell
proliferation. The Raf zinc finger binds to Ras at an
epitope that is available only on prenylated Ras, and is
distinct from the effector loop. In addition to its
30 participation in Ras binding, a role for the zinc finger
in Raf activation is revealed by the loss of Raf-CaaX
transforming activity by mutation of the zinc finger.
Reagents

Phorbol 12, 13 dibutyrate (phorbol myristate

3 5 acetete; PMA) was purchased from Sigma. EGF was

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purchased from Calbiochem. Commercially available
anti-Myc monoclonal antibodies, e.g., 9B7 and 9E10.2,
were employed for immunoprecipitation and immunoblotting.
The M2 Flag monoclonal antibody was purchased from Kodak.
5 Enhanced Chemiluminescence (ECL) reagents were obtained
from Amersham.

c-Raf-l was tagged immediately after the initiator
methionine. DNA encoding a thirty-three amino acid
epitope from human c-Myc was inserted into pMT2 . Human
10 c-Ha Ras (V12) was tagged at its aminoterminus with the
FLAG epitope (MDYKDDDK; SEQ ID NO: 8); DNA encoding the
tag was inserted into the vector pCMV5 (Anderson et al.,
1989, J. Biol. Chem. 264:8222). The c-Ha Ras, human
MEK-1, and rat ERK-1 polypeptides were expressed as GST
15 fusion proteins using the pGEX-KG vector (Guan et al.,

1991, Anal. Biochem. 192:262-276). After purification by
GSH-sepharose, free ERK-1 was obtained by thrombin
cleavage. Human PKCy cDNA was obtained from ATCC
Accession Number 37707.
2 0 Mutagenesis of Raf

The site specific mutations in the Raf
aminoterminus (K 84 ALK (SEQ ID NO: 4) to A 84 AAA (SEQ ID
NO: 9); C165, 168S) were introduced using the Altered
Sites mutagenesis system (Promega) . Replacement of the
25 Raf zinc finger domain by the more car boxy terminal of the
two zinc fingers of PKCy (Fig. 1A-1B) was accomplished as
follows. The Raf zinc finger domain was first removed by
deleting amino acids 150-177 (SEQ ID NO:6). A Raf-l cDNA
fragment encoding amino acids 178-305 was amplified by
30 polymerase chain reaction (PCR) ; the upstream primer used
had the DNA sequence of 5'

AGCT AAGCTT GTAGC GGTACCA AAGTACCTACTATG 3' (SEQ ID NO: 10),

which introduces HindlTX and KpnT sites (restriction
sites are underlined) . The downstream primer used had
35 the DNA sequence of 5' GGGTTTTCGGCTGTGACCAG 3' (SEQ ID

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NO: 11). The amplified cDNA fragment, cut with HindXXX
and BstXI, was used to replace a Raf HindXXX and BstXZ
cDNA segment encoding amino acids 149 to 305. Next, the
DNA sequences encoding the more car boxy terminal zinc
5 finger domain (amino acids 99 to 152 (SEQ ID NO:7) of
human PKC Y were amplified as follows: upstream primer,
5 ' AGCTA£GCITCGGAACAAGCACAAGTTCCGT3 ' ( SEQ ID NO : 1 2 ) ;
downstream primer: 5 ' CGGGGTA£CGCACAGAGAGGGCACGCT3 ' (SEQ
ID NO: 13) (Quest et al., 1994, J. Biol. Chem. 269:2961-
10 2970) . The amplified PKCy zinc finger domain was

inserted into the Raf (a 150-177) mutant at the HindXXX
and KpnX sites to give the y/Raf chimera shown in Fig.
1A-1B. The Raf mutants were confirmed by DNA sequencing.

The Raf CaaX construct was made by subcloning an
15 EcoRX fragment of a cDNA encoding wildtype c-Raf-l into
pAlter (Promega) . The gene was altered to encode a
shortened N-terminal Myc epitope ( MEEQKLI S E EDL ; SEQ ID
NO: 14) and the c-terminal 17 amino acids of K-Ras-4B
(KDGKKKKKKSKTKCVIM; SEQ ID NO: 15) using the Altered Sites
20 mutagenesis system (Promega) . Additional mutations were
later introduced in c-Raf-l using the Myc-Raf CaaX gene
as a template. Mutations were confirmed by DNA
sequencing and by in vitro translation of the mutant gene
using the Promega TNT system. For expression in
25 mammalian cells, DNA encoding Raf CaaX was subcloned as
an EcoRI fragment into the pBAB puro vector.
Transipnt. expression, immunoprecipj tat ions and
jmmunoblots

The cDNAs encoding the Myc-tagged c-Raf-l variants
30 in the mammalian expression vector P MT2 , alone or with a
FLAG-tagged Ha-Ras (V12) in the vector pCMV5, were
transfected into COS M7 cells by the DEAE-dextran method
known in the art using a total of 10 M g of the
recombinant DNA. For the Ras-Raf coprecipitation

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experiments, cells were extracted 48 hours after
transfection into a lysis buffer containing 50 mM Tris Cl
(pH 7.5), 1 mM EDTA, 2 mM EGTA, 1 mM dithiothreitol , 25
mM ^-glycerophosphate, 1 mM sodium vanadate, 1% triton
5 X-100, and proteinase inhibitors. For the measurement of
Raf kinase activity, the cells were serum-deprived by
placement in Dulbeccos modified Eagles minimal essential
medium (DMEM) containing 0.1% FBS. Serum-deprivation of
cells was commenced 30 hours after the cells were
10 transfected. After an additional 16-18 hours, the cells
were treated with 10% FBS, mitogens or carrier (control)

prior to lysis.

Immunoprecipitations were conducted for one hour

at 4°C using monoclonal antibody 9B7 . 3 for Myc-Raf and
15 the M2 anti-FLAG monoclonal antibody for FLAG— Ras . The

immune complexes were recovered with protein-G Sepharose

and subjected to SDS-polyacrylamide gel electrophoresis

followed by electrophoretic transfer to a PVDF membrane.

The resolved proteins were visualized by the ECL method
2 0 known in the art using either anti-Myc monoclonal

antibody 9E10.2 or anti-flag antibody M2.

In vitro binding of Raf Var iants to Ras

The recombinant GST-Ha -Ras polypeptide was

expressed in E. Coli and purified on GSH sepharose. COS

2 5 recombinant FLAG-tagged Ha -Ras (V12) was purified by

immunoprecipitation with the M2 anti-FLAG monoclonal
antibody and protein-G Sepharose. The immobilized Ras
polypeptides were labeled in vitro with S-y-GTP. COS
cell extracts containing recombinant Raf variants were
30 incubated with immobilized Ras at 4°C, for one hour. The
complexes were recovered and washed three times in lysis
buffer and subjected to immunb lotting.
Raf kinase assay

The kinase activities of the immunoprecipitated

3 5 Raf variants was assessed using the coupled kinase assay

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known in the art, e.g., Kyriakis et al., 1993, J. Biol.
Chem. 268:16009-16019. The reaction was carried out in a
two-stage incubation, in a total volume of 100 /il. In
the first stage, the assay mixture contained 2 5 mM
5 Tris-Cl (pH 7.8), 10 mM MgCl 2 , 1 mM DTT, 0.1 mM y 32 P~ATP
(4000 cpm/pmole) , and 2 ng/ml prokaryotic recombinant
GST-MEK1. The reaction was initiated at 30°C by addition
of y 32 P _atp ' After 20 min. , an aliquot of prokaryotic
ERK-1 was added to a final concentration of 10 /ig/ml; the

10 incubation was continued for an additional 30 minutes,

and terminated by addition of SDS sample buffer. The 32 P
incorporation into GST-MEK1 and ERK1 was detected by
autoradiography after SDS-PAGE.
Raf CaaX transforma tion assay

15 Rat-l fibroblasts were maintained in DMEM

supplemented with 10% fetal calf serum (GIBCO) . Cells
grown in a 100 mm dish were transfected with 10 fig of
CsCl-purif ied plasmid DNA using a calcium phosphate
transfection kit (GIBCO) . On day three, 90% of cells

20 were transferred into a 150 mm dish. One-tenth of the

cells were plated in DMEM containing 2.5 /ug/ml puromycin.
Transfected cultures were incubated at 37 °C, 5% C02 for
three weeks. Transformation was evaluated by counting
cell foci, an indication of unwanted cell proliferation,

25 and staining the cells with crystal violet.

Transf ections were standardized by comparing the relative
numbers of puromycin— resistant colonies.

Zinc finger domain mutations affect Raf kin ase activity

To examine the role of the Raf zinc finger domain

30 in Raf function, two variant zinc finger structures were
made. In one, the cysteines at Raf residues 165 and 168
were both converted to serines, thereby mutating both of
the tandem (Cys 3 His) zinc binding structures. A second
variant was constructed by deleting Raf amino acids

35 150-177 (SEQ ID NO: 6) and replacing them with PKCy amino

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acids 99-152. PKCy amino acids 99-152 (SEQ ID NO: 7)
completely encompass -the second, more carboxy tennina 1 of
the two PKCy zinc finger motifs (H 102 to C 151 ) , which like
the Raf zinc finger is another (Cys 3 His) 2 structure (Fig.
5 IB) . The expression and regulation of the mutant Raf
polypeptides (each of which was tagged at the
aminoterminus with a Myc epitope) , was examined during
transient expression in COS cells. All Raf variants
exhibited comparable polypeptide expression, however the

10 level of kinase activity in the mutants differed

substantially from the wild type (Figs. 2A-2D and 3A-3C) .
Wildtype Raf was strongly activated by treatment of cells
with Raf activators, e.g. , EGF or PMA, prior to harvest.
Mutation of the Raf zinc finger (C165, 168S) resulted in

15 little change in basal Raf kinase activity, but inhibited
the EGF and PMA-stimulated activation of Raf kinase by
75-80% (Figs. 2A-2D) . Replacement of the Raf zinc finger
domain with the zinc finger domain of PKCy (y/Raf)
resulted in a slight increase in basal Raf kinase

2 0 activity, but the response to EGF remained profoundly

inhibited. In contrast, phorbol ester, e.g. , PMA,
increased the MEK kinase activity of y/Raf to levels
comparable to those observed in the EGF/ PMA stimulated
wildtype Raf (Figs. 2A-2D and 3A-3C) . The PMA activation
25 of y/Raf is abrogated completely by a double Cys to Ser
mutation of the PKCy zinc finger (Figs. 2A-2D) . The
PMA-stimulated activation of y/Raf was not dependent on
endogenous PMA-responsive PKCs. y/Raf activity remained
elevated throughout a 24 hour PMA treatment of

3 0 transfected COS cells, whereas Myc Raf activity returned

to baseline and was unresponsive to readdition of PMA
(but not EGF) , indicating effective PKC down regulation.
Addition of PMA directly to y/Raf immunoprecipitated from
serum-deprived COS cells did not increase y/Raf activity
35 under conditions in which the rat brain PKC is strongly

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activated. Thus PMA binding to y/Raf in situ is
necessary, but not sufficient for activation of y/Raf.

Experiments were conducted to determine whether
endogenous Ras was essential for the PMA-stimulated
5 activation of y/Raf. Mutation of Raf amino acids K 84 ALK 87
(SEQ ID NO: 4) abolished the ability of a fragment of Raf
containing amino acids 1-149 to bind in vitro to
prokaryotic Ras-GTP. Introduction of the (84-87A)
mutation into wildtype Raf resulted in over 85%
10 inhibition in the EGF or PMA-stimulated activation in COS
cells expressing Myc Raf (84-87A) compared to those
expressing wildtype Myc Raf (Figs. 3A-3C) . When
introduced into y/Raf , the (84-87A) mutation reduced the
residual EGF-stimulated activity by a further 80%, so
15 that the overall activity of the y/Raf (84-87A) variant
in the presence of EGF was less than 5% that of wildtype
Raf. in contrast, the activity of y/Raf (84-87A) in the
presence of PMA was approximately 50% that of wildtype
Raf (Figs. 3A-3C). Thus the ability of PMA to activate
20 y/Raf in situ exhibits little dependence on an
interaction between y/Raf and Ras.

These data indicate that a structurally intact
zinc finger is necessary for Raf activation by receptor
tyrosine kinases. Replacement of the Raf zinc finger by
25 a homologous zinc finger structure is not sufficient to
restore normal regulation by receptor tyrosine kinases,
even though the replacement zinc finger and the Raf
catalytic domain are themselves functionally intact.

»f sine ^rr^r- domain mutations on the binding of

30 Raf to Ras

The loss of EGF-stimulated Raf activation caused

by a site mutation or replacement of the Raf zinc finger

was found to be almost as severe as the inhibition caused

by mutation of Raf residues 84-87 (SEQ ID NO: 4) in the

3 5 Ras-binding domain which binds directly to the effector

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loop of Ras. The association in situ of Ha Ras (V12)
with wildtype and variant Rafs was evaluated by
coimmunoprecipitation experiments (Pigs. 4A-4C) .
Recovery of Myc-Raf (84-87A) with Ha -Ras (V12) was
5 decreased to less than 10% of that of wildtype Myc-Raf.
Recovery in the Ras immunoprecipitate of the zinc finger
variants Raf (C165/168S) and Myc-y/Raf was also
substantially decreased, to approximately 20-25% of the
level observed with wildtype Myc-Raf.

10 The impaired ability of the Raf zinc finger

variants to bind to Ras in situ was confirmed by
examination of the binding in vitro (Figs. 5A-5B) .
Recombinant v-Ha Ras was expressed alone in COS cells,
purified by immunoprecipitation, and incubated in vitro

15 with extracts from COS cells transfected with wildtype
Raf, Raf (84-87A) , y/Raf, and a double mutant y /Raf
(84-87A) . In parallel to the results observed with
coexpression in situ (Figs. 4A-4C) , the binding of y/Raf
to COS recombinant v-Ha Ras in vitro is substantially

2 0 decreased compared to wildtype Raf, and the binding of

Raf (84-87A) to Ras even more so. No binding was
detected with the Raf double mutant (Fig. 5A-5B) . The
impaired binding of Raf zinc finger mutants to Ras was
unexpected because binding of GST Raf 1-149 and GST Raf

25 1-257 to prokaryotic Ras-GTP was essentially
indistinguishable .

The ability of COS recombinant Raf, Raf
(C165/165S) , y/Raf and Raf (84-87A) to bind in vitro to
prokaryotic GST— Ras— GTP was examined (Figs. 6A-6B) . Raf

30 (84-87A) exhibited impaired binding to GST— Ras— GTP

compared to the binding observed with wildtype Raf. In
contrast, the prokaryotic Ras GTP bound to the zinc
finger mutant Rafs at a level comparable to the binding
of wildtype Raf. These data indicate that optimal Raf

3 5 binding to prokaryotic, unprenylated GST— Ras-GTP does not

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require an intact Raf zinc finger, whereas the binding of
Raf to COS recombinant Ras, which undergoes
carboxyterminal prenylation and processing in situ, is
strongly dependent on the integrity of the Raf zinc
5 finger, whether examined in vitro, or during coexpression
in situ.

B ff C rt s of zinc fincrer domain mutation on the biologic

activity of Raf CaaX

The role of the Raf zinc finger in Raf activation,
10 e.g., Ras binding and the translocation of Raf to the
membrane, was examined. The effects of zinc finger
mutation on the ability of Raf CaaX to promote focus
formation, i.e., cell proliferation, is shown in TABLE 1.

TABLE 1

15 Tr^nsformaHnn of Ra f -i fibroblasts by Raf CaaX js

Sig^SfeS T„ r .irai bv Mnt.nt.1on of th* We FrngS

Construct Focus Formation Raf CaaX Expression

pBAB puro (vector) 0 No

Raf CaaX, wildtype 100 jej
20 Raf CaaX, K375M 0 <efo

Yes

Raf CaaX, K84ALK- 64 +/- 23

A84AAA , , ^ v __

Raf CaaX, C165,168S 15 +/- 12 *es

Rat-1 cells were transfected with 10 of
2 5 pBABpuro plasmid DNA encoding each of the Raf mutants.
Foci formation was standardized to wildtype Raf CaaX
which was approximately 50% as efficient as HRas (V12)
expressed in pBABpuro. Results are the average of five
independent experiments.

30 Raf CaaX has been engineered to express Ki-Ras

residues 172 to 188 (SEQ ID NO: 15) fused to the Raf
carboxyterminus. The Raf CaaX fusion protein undergoes
prenylation and other carboxyterminal processing
characteristics of Ki-Ras, which are involved in the

35 constitutive localization of Raf CaaX at the cell surface

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membrane. In contrast to unmodified c-Raf-1, Raf CaaX is
a potent transforming agent in rat-1 cells, resulting in
focus formation at approximately 50% the rate of
oncogenic Ha-Ras (V12) - Mutation at the Raf ATP binding
5 site (K375M) completely abolished the transforming

activity of Raf CaaX (TABLE 1) . Mutations throughout the
Raf aminoterminus that abolish the binding of GST Raf
1-149 prokaryotic Ras-GTP in vitro and which strongly
inhibit the EGF/PMA activation of wildtype Raf (Figs. 1A-

10 IB and 2A-2D) had no significant effect on the number of
foci formed by Raf CaaX. These data indicate that
transformation by Raf CaaX is independent of its ability
to bind to the Ras effector domain. In contrast,
mutation of the Raf CaaX zinc finger domain inhibited

15 focus formation by 85% (TABLE 1) . This result suggests
that a structurally intact zinc finger domain is
necessary for Raf kinase activity in situ, irrespective
of prior Raf recruitment to the plasma membrane.
Raf protein domains involved in binding to Ras

20 The manner in which Raf interacts with Ras was

characterized. Binding assays, competitive co-
precipitation assays, and kinase assays were used to
measure Ras-Raf binding and activation of Raf kinase.

The consequences of Raf zinc finger mutation, e.g,

25 site mutations or replacement of the Raf zinc finger with
the PKC zinc finger) are not due to a propagated
disturbance in the folding of other important functional
domains in the Raf polypeptide. The integrity of the Raf
catalytic domain was verified in the y/Raf mutant, the

30 kinase activity of which, although poorly responsive to
EGF, is activated fully by PMA. This result also
validates the functional integrity of the PKCy zinc
finger, expressed as a fusion within the Raf polypeptide.
The functional integrity of the aminoterminal Raf

35 segment, residues 50-150 (SEQ ID NO: 5), was confirmed by

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the data shown in Figs. 6A-6B, which demonstrate that the
binding of Raf (C165, 168S) and y/Raf to prokaryotic
GST-Ras-GTP is essentially identical to that of wildtype
Raf. Consequently, the altered response of Raf (C165,
168S) and v/Raf to EGF in situ is attributable to loss of
functions provided by the normal Raf zinc finger
structure, rather than to disturbances elsewhere in the
Raf polypeptide introduced by the mutation.

The mechanisms of PMA activation of wildtype Raf
and the y/Raf are largely distinct. PMA activation of
wildtype Raf proceeds through the PMA-induced activation
of Ras. Mutation of Raf residues 84-87 (SEQ ID NO: 4) in
wildtype Raf reduces PMA activation by greater than 85%,
whereas such a mutation has less of an impact on PMA
15 activation of y/Raf . PMA activation of y/Raf depends on
direct binding of PMA to y/Raf, as evidenced by the
abrogation of the activation by mutation of the PKCy zinc
finger within y/Raf (Figs. 2A-2D) . In contrast, PMA
activation of wildtype Raf is entirely indirect; PMA does
2 0 not bind directly to the Raf zinc finger.

The insertion of the PKCy zinc finger in place of
the normal Raf zinc finger serves both to eliminate the
functions of the normal Raf zinc finger, and to introduce
a new set of functions, defined by those of the PKCy zinc
25 finger. One newly acquired function is the ability of
y/Raf to bind PMA directly, thereby enabling the
Ras-dependent membrane localization step to be bypassed,
at least in the presence of PMA; like the addition of a
CaaX motif to Raf, the PKCy zinc finger enables the
30 recruitment of Raf to the membrane in the presence of PMA
to proceed in a Ras-independent fashion. The binding of
PMA to y/Raf in itself does not directly activate Raf,
but like the addition of CaaX to the Raf carboxyterminus ,
the PKCY zinc finger enables the steps necessary for Raf
35 activation to proceed effectively.

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As discussed above, the Raf zinc finger structure
participates in the regulation of the Raf kinase activity
in at least two ways. First, the Raf zinc finger is
critical for the high affinity association of Raf with
5 Ras in situ. The interaction of the Raf zinc finger with
Ras appears to be independent of the interaction between
the Ras effector loop and the more aminoterminal Raf
segment (amino acids 50-150) . The latter interaction is
disrupted by mutation of Raf residues 84-87, which

10 greatly reduces the binding in vitro of Raf to

prokaryotic, unprenylated GST— Ras— GTP . In contrast,
mutation in, or replacement of the Raf zinc finger does
not detectably alter Raf binding to prokaryotic GST—
Ras— GTP, but only to eukaryotically expressed, prenylated

15 Ras.

The site on Ras to which the Raf zinc finger binds
involves Ras residues, e.g., Ras N26, V45, that flank the
effector loop. Ras prenylation also contributes to the
binding of Ras with the Raf zinc finger. The

20 contribution to Ras-Raf binding from the Raf zinc finger
likely increases the avidity of Raf binding to the
membrane, either to Ras itself or to acidic phospholipids
in the membrane inner leaflet. In addition, the Raf zinc
finger participates in the steps that lead to activation

25 of Raf catalytic function. A second function of the

zinc finger in the transition of Raf from inactive to an
active state is indicated by the inhibitory effect of
zinc finger mutation on the transforming action of Raf
CaaX. Fusion of the carboxyterminal CaaX motif from

30 Ki-Ras onto c-Raf is sufficient to target Raf to the
plasma membrane, where it undergoes a Ras-independent
activation, and is capable of Ras-independent
transformation of rat-1 cells. Mutation of the zinc
finger markedly impairs the transforming activity of Raf

35 Caax (TABLE 1) . These results indicate that once at the

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plasma membrane, an intact Raf zinc finger is required
for a subsequent step in Raf activation. The binding of
PMA may induce a conformational change in y/R af that
enables y /Raf to be converted to an active state through

5 a covalent modification (e.g., a site specific

phosphorylation or acylation) of the y/Raf polypeptide.
The Raf zinc finger may also mediate an analogous step in
the activation of membrane-bound Raf CaaX, as well as in
the activation of wildtype c-Raf-l bound to Ras-GTP in

0 situ

The role of the Raf zinc finger in Raf activation
involves the binding of the zinc finger to a membrane
associated lipid, e.g., the farnesyl moiety of Ras
itself. Engagement of the Raf zinc finger by the prenyl

5 moiety or another membrane lipid induces a conformational
change in c-Raf-l that enables a further, covalent
modification which results in stable activation of Raf
catalytic activity. The direct binding of the Ras prenyl
structure or other lipids to Raf is a crucial step in

0 c-Raf-l activation. The Raf zinc finger domain binds to
an epitope present only in prenylated Ras.

Figs 7A-B show that a bacterial recombinant fusion
protein (GST, Raf 130-220) that encompasses the Raf zinc
finger domain (SEQ ID NO: 2) binds strongly to processed

5 (i.e., f arnesylated) baculoviral (BV) recombinant H-Ras
but very poorly to unprocessed (i.e., unf arnesylated) BV
H-Ras. These data indicate that zinc finger domain-
mediated Ras-Raf binding is dependent on Ras
farnesylation, i.e., Ras processing, (and is not GTP—

0 dependent) . In contrast, the association of Raf amino
acids 50-150 (SEQ ID NO: 5) to the Ras effector loop (Ras
residues 32-40; SEQ ID NO: 3) is GTP-dependent .
Therapeutic appli cations

The methods of the invention are useful in

5 treating diseases characterized by unwanted proliferation

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of cells. The invention provides methods of inhibiting
Ras-Raf binding interaction by administering compounds,
e.g. , inhibitory fragments of Ras or Raf (or analogs
thereof) , or small molecules the structure of which is
5 modeled after the structure of inhibitory polypeptides.

A "fragment" will ordinarily be at least about 10
amino acids, usually about 20 contiguous amino acids,
preferably at least 4 0 contiguous amino acids, more
preferably at least 50 contiguous amino acids, and most

10 preferably at least about 60 to 80 or more contiguous

amino acids in length. Such peptides can be generated by
methods Known to those skilled in the art, including
proteolytic cleavage of the protein, de novo synthesis of
the fragment, or genetic engineering.

15 Analogs can differ from the native peptides of Ras

or Raf by amino acid sequence, or by modifications which
do not affect the sequence, or by both. Preferred
analogs include peptides whose sequences differ from the
wild-type sequence (i.e., the sequence of the homologous

20 portion of the naturally occurring peptide) only by

conservative amino acid substitutions, preferably by only
one, two, or three, substitutions, for example,
substitution of one amino acid for another with similar
characteristics (e.g., valine for glycine, arginine for

2 5 lysine, etc.) or by one or more non-conservative amino

acid substitutions, deletions, or insertions which do not
abolish the peptide's biological activity.

Modifications (which do not normally alter primary
sequence) include in vivo or in vitro chemical
30 derivitization of peptides, e.g., acetylation or
carboxylation. Also included are modifications of
gly cosy lat ion, e.g., those made by modifying the
glycosylation patterns of a peptide during its synthesis
and processing or in further processing steps, e.g., by

3 5 exposing the peptide to enzymes which affect

glycosylation e.g., mammalian glycosylating or

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deglycosylating enzymes. Also included are sequences
which have phosphorylated amino acid residues, e.g.,
phosphotyrosine, phosphoserine, or phosphothreonine .

The invention includes analogs in which one or
5 more peptide bonds have been replaced with an alternative
type of covalent bond (a "peptide mimetic") which is not
susceptible to cleavage by peptidases. Where proteolytic
degradation of the peptides following injection into the
subject is a problem, replacement of a particularly
10 sensitive peptide bond with a noncleavable peptide

mimetic will make the resulting peptide more stable and
thus more useful as a therapeutic. Such mimetics, and
methods of incorporating them into peptides, are well
known in the art. Similarly, the replacement of an L-
15 amino acid residue is a standard way of rendering the
peptide less sensitive to proteolysis. Also useful are
amino-terminal blocking groups such as t-
butyloxycarbonyl, acetyl, theyl, succinyl,
methoxysuccinyl, suberyl, adipyl, azelayl, dansyl,
20 benzyloxycarbonyl, f luorenylmethoxy car bony 1,

methoxyazelayl, me thoxy adipyl, methoxy suberyl , and 2,4,-
dinitrophenyl . Blocking the charged amino- and carboxy-
termini of the peptides would have the additional benefit
of enhancing passage of the peptide through the
25 hydrophobic cellular membrane and into the cell.

Modification of these peptides to improve
penetration of the blood-brain barrier would also be
useful. Peptides may be altered to increase
lipophilicity (e.g. by esterif ication to a bulky
30 lipophilic moiety such as cholesteryl) or to supply a
cleavable "targetor" moiety that enhances retention on
the brain side of the barrier (Bodor et al. , Science
1992, vol. 257, pp. 1698-1700). Alternatively, the
peptide may be linked to an antibody specific for the
35 transferrin receptor, in order to exploit that receptor's

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role in transporting iron across the blood-brain barrier
(Friden et al., Science . 1993, vol. 259, pp. 373-377).

Peptides may be administered to the patient
intravenously in a pharmaceutically acceptable carrier
5 such as physiological saline. Standard methods for
intracellular delivery of peptides can be used, e.g.
delivery via liposomes. Such methods are well known to
those of ordinary skill in the art. The formulations of
this invention are useful for parenteral administration,

10 such as intravenous, subcutaneous, intramuscular, and
intraperitoneal.

Since blocking the association of Ras with Raf
interferes with receptor-mediated activation of immune
cells, this method may also be useful in downregulating

15 the immune response in patients with autoimmune diseases
such as systemic lupus erythematosus (SLE) , type 1
diabetes, and rheumatoid arthritis. Suppression of an
immune response using this method may also be useful in
the treatment of allograft or xenograft recipients to

2 0 prevent rejection of a transplanted organ.

Therapeutic administration of a peptide
intracellular ly can also be accomplished using gene
therapy, wherein a nucleic acid which includes a promoter
operatively linked to a sequence encoding a heterologous

25 peptide is used to generate high-level expression of the
peptide in cells transfected with the nucleic acid. DNA
or isolated nucleic acid encoding peptides of the
invention may be introduced into cells of the patient by
standard vectors and/or gene delivery systems. Suitable

30 gene delivery systems may include liposomes, receptor-
mediated delivery systems, naked DNA, and viral vectors
such as herpes viruses, retroviruses, and adenoviruses,
among others .

Pharmaceutically acceptable carriers are

35 biologically compatible vehicles which are suitable for
administration to an animal: e.g., physiological saline.

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A therapeutically effective amount is an amount of the
nucleic acid of the invention which is capable of
producing a medically desirable result in a treated
animal .

5 As is well known in the medical arts, dosages for

any one patient depends upon many factors, including the
patient's size, body surface area, age, the particular
compound to be administered, sex, time and route of
administration, general health, and other drugs being
10 administered concurrently. Dosages for the compounds of
the invention will vary, but a preferred dosage for
intravenous administration is from approximately 10 6 to
10 22 copies of the nucleic acid molecule in the case of
gene therapy.

15 compounds that inhibit the inter action of Pas with Raf

Investigations of the respective binding surfaces
of the Raf and Ras proteins has shown that in addition
to the binding of the Ras effector loop (amino acids 32-
40) to Raf amino acids 50-150, the Raf zinc finger domain

2 0 is essential for Ras-Raf binding. Inhibitory peptides,
can be used as models to synthesize therapeutic compounds
which inhibit Ras/Raf interaction in vitro and in vivo.
Such modeling techniques are known in the art of
synthetic chemistry.

25 For example, small, overlapping sets of amino acid

peptides which span the regions of Raf residues 50-150
and 139-184 and Ras residues 32-40 can be synthesized and
screened for inhibitory activity. Peptides found to
inhibit Ras-Raf interaction can then be used as

30 structural prototypes for the synthesis of

conformationally constrained analogs. Peptide bonds
within the analogs can be modified or replaced to yield
potent, stable, non-peptidyl inhibitors suitable for
therapy.

35 The crystal structure of Ras is known in the art

and can thus be used to derive the actual conformation of

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binding residues. Similarly, X-ray crystallography of
Raf crystals and Ras/Raf co-crystals can be used to
predict the inhibitory structure of each inhibitory
peptide. The structure of the Raf -derived inhibitory
5 peptides can be used to formulate smaller non-peptidyl
compounds which mimic essential aspects of the
interactive peptide structure. The inhibitory activity
of these candidate compounds can then be confirmed using
the methods of the invention.

10 Co-crystals of peptide-Ras and peptide-Raf can be

analyzed using X-ray crystallography and nuclear magnetic
resonance analysis to determine the structure of the
inhibitory peptide in its bound state. Inhibitory
peptides can also be characterized by physical chemistry

15 techniques, e.g., circular dichroism, fluorescence,

electron spin resonance, that yield data concerning the
local environment of the peptides interacting with the
protein. Synthetic chemistry techniques can then be used
as described above to produce compounds which mimic the

2 0 inhibitory conformation of each peptide.

Screening assays

The invention can also be used to screen a
candidate compound for the ability to inhibit the
interaction of Ras with Raf.
25 Candidate compounds can be evaluated for anti-

proliferative activity by contacting Raf or a Ras-binding
fragment thereof, e.g., a zinc finger domain-containing
fragment of Raf, with a candidate compound and
determining binding of the candidate compound to the

3 0 peptide, or Ras-Raf binding. Raf or Ras-binding fragment

of Raf can be immobilized using methods known in the art
such as binding a GST-Raf fusion protein to a polymeric
bead containing glutathione. Binding of the compound to
the Raf peptide is correlated with the ability of the
35 compound to disrupt the signal transduction pathway and
thus inhibit cell proliferation.

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A co-precipitation competition assay can also be
used to measure the relative binding affinities of Ras or
fragments and mutants thereof for Raf and fragments and
mutants thereof. The effect of various candidate
5 compounds to disrupt or reduce binding can also be
measured in such a competition assay.

Candidate compounds can be screened for the
ability to bind to Ras or a Raf -binding fragment of Ras.
Similarly, compounds can be screened as above for the

10 ability to bind to Raf to identify a compound with anti-
proliferative activity.

In another screening method, one of the components
of the Ras-Raf binding complex, such as Ras or a Raf-
binding fragment of Ras or Raf or a Ras-binding fragment

15 of Raf, is immobilized. Peptides can be immobilized

using methods known in the art, such as adsorption onto a
plastic microtiter plate or specific binding of a GST-
fusion protein to a polymeric bead containing
glutathione. For example, GST— Raf or GST-Ras can be

20 bound to glutathione-Sepharose beads. The immobilized
peptide is then contacted with the labeled peptide to
which it binds (Ras in this case) in the presence and
absence of a candidate compound. Unbound peptide can
then be removed and the complex solubilized and analyzed

2 5 to determine the amount of bound labeled peptide. A

decrease in binding is an indication that the candidate
compound inhibits the interaction of Ras with Raf.

A variation of the above-described screening
method can be used to screen for another class of

3 0 candidate compounds which are capable of disrupting a

previously-formed Ras-Raf interaction. In this example,
a complex comprising Ras or a Raf -binding fragment
thereof bound to Raf or a Ras-binding fragment thereof is
immobilized as described above and contacted with a
35 candidate compound. The dissolution of the complex by

the candidate compound correlates with the ability of the

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candidate compound to disrupt or inhibit the interaction
of Ras with Raf.

Another screening method involves measuring Raf
activation or Raf catalytic activity, e.g. , Raf kinase
5 activity, in the presence and absence of a candidate
compound. A decrease in Raf activation in the presence
of the compound compared to that in its absence is an
indication that the candidate compound inhibits Raf
activation, and therefore, signal transduction along the

10 Ras-Raf pathway.

In yet another screening assay, candidate
compounds can be screened for the ability to inhibiting
cell proliferation by providing a cell transfected with
DNA encoding a transformation-competent Ras such as

15 Ha-Ras (V12) , Ras CaaX, or myristoylated Ras (Cadwallader
et al., 1994, Mol. Cell. Biol. 14:4722-4730); contacting
the cell with a candidate compound; and determining the
amount of proliferation of the cell. Cells transfected
with transformation-competent proliferate to form foci in

20 culture. A decrease the number of foci in the presence
of the candidate compound compared to that in the absence
of the candidate compound indicates that the candidate
compound inhibits cell proliferation.

Raf CaaX and myristoylated Raf are Ras-

25 independent, i.e., these constructs do not require the
effector loop of Ras to localize to the cell membrane.
Thus, using cells transfected with DNA encoding Raf CaaX
or aminoterminal myristoylated Raf in the screening assay
identifies compounds that disrupt the function of the

3 0 zinc finger in Raf activation which results in a decrease
in foci formation or cell proliferation.

Other embodiments are within the following claims.

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SEQUENCE LISTING

(1) GENERAL INFORMATION

(i) APPLICANT: The General Hospital Corporation and
Indiana University Foundation

5 (ii) TITLE OF THE INVENTION: INHIBITING PROTEIN INTERACTIONS

(iii) NUMBER OF SEQUENCES: 18

(iv) CORRESPONDENCE ADDRESS :

(A) ADDRESSEE: Fish & Richardson, P.C.

(B) STREET: 225 Franklin Street
10 (C) CITY: Boston

( D ) STATE : MA

(E) COUNTRY: US

(F) ZIP: 02110-2804

(v) COMPUTER READABLE FORM:
15 (A) MEDIUM TYPE : Diskette

(B) COMPUTER: IBM Compatible

(D) SOFTWARE: FastSEQ for Windows Version 2.0

(vi) CURRENT APPLICATION DATA:
20 (A) APPLICATION NUMBER:

(B) FILING DATE: ll-MAR-1997

(vii) PRIOR APPLICATION DATA:

(A) APPLICATION NUMBER: 60/013,274
25 (B) FILING DATE: 12-MAR-1996

(viii) ATTORNEY /AGENT INFORMATION:

(A) NAME: Fraser, Janis K.

(B) REGISTRATION NUMBER: 34,819

30 (ix) TELECOMMUNICATION INFORMATION :

(A) TELEPHONE: 617-542-5070

(B) TELEFAX: 617-542-8906

(2) INFORMATION FOR SEQ ID NO:l:

(i) SEQUENCE CHARACTERISTICS:
35 (A) LENGTH: 46 amino acids

(B) TYPE: amino acid
( d ) TOPOLOGY : 1 inear

(ii) MOLECULE TYPE: None

(xi) SEQUENCE DESCRIPTION: SEQ ID NO:l:

40 His Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Cys Xaa Xaa
i 5 l 0

Cys Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Cys Xaa Xaa Cys Xaa Xaa

20 25 30

Xaa Xaa His Xaa Xaa Cys Xaa Xaa Xaa Xaa Xaa Xaa Xaa Cys

45 35 40 43

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(2) INFORMATION FOR SEQ ID NO: 2:

(i) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 46 amino acids

(B) TYPE: amino acid
(D) TOPOLOGY: linear

(ii) MOLECULE TYPE: None

(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 2:

His Asn Phe Ala Arg Lys Thr Phe Leu Lys Leu Ala Phe Cys Asp lie

1 5 10 15

Cys Gin Lys Phe Leu Leu Asn Gly Phe Arg Cys Gin Thr Cys Gly Tyr

20 25 " 30

Lys Phe His Glu His Cys Ser Thr Lys Val Pro Thr Met Cys
35 40 45

(2) INFORMATION FOR SEQ ID NO: 3:

(i) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 9 amino acids

(B) TYPE: amino acid
(D) TOPOLOGY: linear

(ii) MOLECULE TYPE: None

(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 3:

Tyr Asp Pro Thr lie Glu Asp Ser Tyr
1 5

(2) INFORMATION FOR SEQ ID NO: 4:

(i) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 4 amino acids

(B) TYPE: amino acid
(D) TOPOLOGY: linear

(ii) MOLECULE TYPE: None

(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 4:

Lys Ala Leu Lys
1

(2) INFORMATION FOR SEQ ID NO: 5:

(i) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 101 amino acids

(B) TYPE: amino acid
(D) TOPOLOGY: linear

(ii) MOLECULE TYPE: None

(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 5:

Asp Pro Ser Lys Thr Ser Asn Thr lie Arg Val Phe Leu Pro Asn Lys

15 10 15

Gin Arg Thr Val Val Asn Val Arg Asn Gly Met Ser Leu His Asp Cys
20 25 30

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Leu Met Lys Ala Leu Lys Val Arg Gly Leu Gin Pro Glu Cys Cys Ala

35 40 45

Val Phe Arg Leu Leu His Glu H1b Lys Gly Lys Lys Ala Arg Leu Asp
cn 55
5 Trp Asn Thr Asp Ala Ala Ser Leu He Gly Glu Glu Leu Gin Val Asp
/:u 70 ,_

Phe Leu Asp His Val Pro Leu Thr Thr His Asn Phe Ala Arg Lys Thr

85 90 "

Phe Leu Lys Leu Ala
10 ioo

(2) INFORMATION FOR SEQ ID NO: 6:

(i) SEQUENCE CHARACTERISTICS :

(A) LENGTH : 28 amino acids

(B) TYPE: amino acid
15 (D) TOPOLOGY: linear

(ii) MOLECULE TYPE: None

(xi) SEQUENCE DESCRIPTION: SEQ ID NO:6:

Ala Phe Cys Asp He Cys Gin Lys Phe Leu Leu Asn Gly Phe Arg Cys

1 5 10 xt3

20 Gin Thr Cys Gly Tyr Lys Phe His Glu His Cys Ser
20 25

(2) INFORMATION FOR SEQ ID NOt7:

(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 55 amino acids

25 (B) TYPE: amino acid

(D) TOPOLOGY : linear

(ii) MOLECULE TYPE: None

(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 7:

Arg Asn Lys His Lys Phe Arg Leu His Ser Tyr Ser Ser Pro Thr Phe

30 cys Asp His Cys cly Ser Leu Leu Tyr Gly Leu Val His Gin Gly Gly

20 — -

Met Lys Cys Ser Cys Cys Glu Met Asn Val His Arg Arg Cys Val Arg
35 40 45

3 5 Ser Val Pro Ser Leu Cys Gly

50 55

(2) INFORMATION FOR SEQ ID NO: 8:

(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 8 amino acids

4 0 (B) TYPE: amino acid

(D) TOPOLOGY: linear

(ii) MOLECULE TYPE: None

(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 8:

Met Asp Tyr Lys Asp Asp Asp Lys
45 1 * 5

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(2) INFORMATION FOR SEQ ID NO: 9:

(i) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 4 amino acids

(B) TYPE: amino acid
5 (D) TOPOLOGY: linear

(ii) MOLECULE TYPE: None

(xi) SEQUENCE DESCRIPTION: SEQ ID NO:9:

Ala Ala Ala Ala
1

(2) INFORMATION FOR SEQ ID NO: 10:

(i) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 36 base pairs

(B) TYPE: nucleic acid

(D) TOPOLOGY: linear

(ii) MOLECULE TYPE: Genomic DNA

(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 10:
AGCTAAGCTT GTAGCGGTAC CAAAGTACCT ACTATG

(2) INFORMATION FOR SEQ ID NO: 11:

20 (i) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 20 base pairs

(B) TYPE: nucleic acid

( D ) TOPOLOGY : 1 inear

25 (ii) MOLECULE TYPE: Genomic DNA

(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 11:
GGGTTTTCGG CTGTGACCAG

(2) INFORMATION FOR SEQ ID NO: 12:

(i) SEQUENCE CHARACTERISTICS:
30 (A) LENGTH: 31 base pairs

(B) TYPE: nucleic acid

( D ) TOPOLOGY : 1 inear

(ii) MOLECULE TYPE: Genomic DNA

35 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 12:

AGCTAAGCTT CGGAACAAGC ACAAGTTCCG T 31

(2) INFORMATION FOR SEQ ID NO: 13:
(i) SEQUENCE CHARACTERISTICS:

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- 34 -

(A) LENGTH: 27 base pairs

(B) TYPE: nucleic acid

(D) TOPOLOGY: linear

5 (ii) MOLECULE TYPE: Genomic DNA

{xi) SEQUENCE DESCRIPTION: SEQ ID NO: 13:
CGGGGTACCG CACAGAGAGG GCACGCT 27

(2) INFORMATION FOR SEQ ID NO: 14:

(i) SEQUENCE CHARACTERISTICS:
10 (A) LENGTH: 12 amino acids

(B) TYPE: amino acid
( D > TOPOLOGY : 1 inear

(ii) MOLECULE TYPE: None

(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 14:

15 Met Glu Glu Gin Lys Leu lie Ser Glu Glu Asp Leu
15 10

(2) INFORMATION FOR SEQ ID NO: 15:

(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 17 amino acids

2 0 (B) TYPE: amino acid

( D ) TOPOLOGY : 1 inear

(ii) MOLECULE TYPE: None

(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 15:

Lys Asp Gly Lys Lys Lys Lys Lys Lys Ser Lys Thr Lys Cys Val lie

25 1 5 10 15

Met

(2) INFORMATION FOR SEQ ID NO: 16:

(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 52 amino acids

3 0 (B) TYPE: amino acid

( D ) TOPOLOGY : 1 inear

(ii) MOLECULE TYPE: None

(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 16:

His Asn Phe Ala Arg Lys Thr Phe Leu Lys Leu Ala Phe Cys Asp lie
35 1 5 10 15

Cvs Gin Lvs Phe Leu Leu Asn Gly Phe Arg Xaa Xaa Xaa Xaa Cys Gin

20 25 30

Thr Cvs Glv Tyr Lys Phe His Glu His Cys Ser Thr Lys Val Pro Thr
35 40 45

40 Met Cys Val Asp
50

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- 35 -

(2) INFORMATION FOR SEQ ID NO: 17:

(i) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 57 amino acids

(B) TYPE: amino acid
5 (D) TOPOLOGY: linear

(ii) MOLECULE TYPE: None

(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 17:

Leu Arg Asn Lys His Lys Phe Arg Leu His Ser Tyr Ser Ser Pro Thr
1 5 10 15

10 Phe Cys Asp His Cys Gly Ser Leu Leu Tyr Gly Leu Val His Gin Gly
20 25 30

Met Lys Cys Ser CyB Cys Glu Met Asn Val His Arg Arg Cys Val Arg

35 40 45

Ser Val Pro Ser Leu Cys Gly Val Asp
15 50 55

(2) INFORMATION FOR SEQ ID NO: 18:

(i) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 91 amino acids

(B) TYPE: amino acid
20 (D) TOPOLOGY: linear

(ii) MOLECULE TYPE: None

(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 18:

Phe

Leu

Asp

His

val

Pro

Leu

Thr

His

Asn

Phe

Ala

Arg

Lys

Thr

Phe

Leu

Lys

Leu

Ala

Phe

Cys

Asp

Cys

Gin

Lys

Phe

Leu

Asn

Gly

Phe

Arg

Cys

Gin

Thr

Cys

Gly

Tyr

Lys

Phe

His

Glu

His

Cys

ser

Thr

Lys

Val

Pro

Thr

Met

Cys

Val

Asp

Trp

Ser

Asn

lie

Arg

Gin

Leu

Phe

Pro

Asn

Ser

Thr

Gly

Asp

Ser

Gly

Val

Pro

Ala

Leu

Pro

Ser

Leu

Thr

Met
85

Arg

Met

Arg

Glu
90

Ser

35 What is claimed is:

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1. A method of reducing proliferation of cells in
a mammal, said method comprising administering to said
mammal, or contacting said cells with, a compound which
inhibits direct binding of a non-effector loop domain of
Ras with a zinc finger domain of Raf.

2. The method of claim 1, wherein said compound
is a zinc finger domain-containing polypeptide.

3. The method of claim 2, wherein said
polypeptide comprises SEQ ID NO: 1.

4. The method of claim 3, wherein said
polypeptide comprises SEQ ID NO: 2.

5. The method of claim 1, wherein said compound
comprises a lipid moiety which binds to a zinc finger
domain of Raf.

6. The method of claim 5, wherein said lipid
moiety is a farnesyl moiety.

7. The method of claim 6, wherein said compound
comprises a carboxyterminal fragment of Ras comprising a
farnesyl moiety at position C 186 .

8. The method of claim 1, further comprising
administering to said mammal, or contacting said cell
with, a second, different compound which inhibits direct
binding of the effector loop domain of Ras with an amino-
terminal Ras-binding domain of Raf.

9. The method of claim 8, wherein said compound
is a polypeptide comprising SEQ ID NO: 3.

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- 37 -

10. The method of claim 8, wherein said compound
is a polypeptide comprising SEQ ID NO: 4.

11. The method of claim 10 , wherein said
polypeptide comprises SEQ ID NO: 5.

5 12. The method of claim 1, wherein said compound

reduces Raf enzymatic activity.

13. The method of claim 1, wherein said mammal is

a human.

14 . A method of determining whether a candidate
10 compound is capable of inhibiting direct binding of Ras

to Raf, comprising

(a) providing a zinc finger domain-containing
fragment of Raf;

(b) providing a Raf -binding fragment of Ras;

15 (c) contacting said zinc finger domain-containing

fragment of Raf or said Raf-binding fragment of Ras with
said candidate compound;

(d) determining the binding of said zinc finger
domain-containing fragment of Raf and said Raf-binding

2 0 fragment of Ras, wherein a decrease in binding in the

presence of said compound compared to that in the absence
of said compound indicates that said compound inhibits
direct binding of Ras to Raf.

15. The method of claim 14, wherein said zinc
2 5 finger domain-containing fragment of Raf comprises the

amino acid sequence of SEQ ID NO: 1.

16. The method of claim 15, wherein said zinc
finger domain-containing fragment of Raf comprises the
amino acid sequence of SEQ ID NO: 2.

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- 38 -

17. The method of claim 14, wherein said Raf-
binding fragment of Ras comprises a farnesyl moiety.

18. The method of claim 5, wherein said farnesyl
moiety is at position C 186 .

19. A method of determining whether a candidate
compound is capable of inhibiting Raf activation,
comprising

(a) providing a fragment of Raf comprising a zinc
finger domain and a kinase catalytic domain;

(b) providing a Raf -binding fragment of Ras;

(c) contacting said zinc finger domain-containing
fragment of Raf or said Raf-binding fragment of Ras with
said candidate compound; and

(d) determining the Raf kinase activity of said
5 fragment of Raf, wherein a decrease in activity in the

presence of said compound compared to that in the absence
of said compound indicates that said compound inhibits
Raf activation.

20. A method of determining whether a candidate
0 compound is capable of inhibiting cell proliferation,

comprising

(a) providing a cell trans fected with a
substantially pure DNA encoding a transf ormation-

competent Ras ;
5 (b) contacting said cell with said candidate

compound ; and

(c) determining the amount of proliferation of
said cell, wherein a decrease in the presence of said
candidate compound compared to the amount in the absence
0 of said candidate compound indicates that said candidate
compound inhibits cell proliferation.

WO 97/34146

PCTVUS97/03881

1/8

U
0*

rH
I

«
OS
I

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PCT/US97/03881

4000 -i

Raf kinase
activity
(32p into Erk-1)
cpm

Raf variants: 1 234 5 6 7 8 9 10 11 12

WTRaf

♦

Raf(C165.168S)

PKCy/Raf

PKCt<H1 02N;C151 S)/Raf

♦

Cell treatment:

Minus serum

♦

Plus EGF

♦

Plus TPA

♦

FIG. 2A

3/8

3 2 P-Po»y peptides

FIG. 2B

Immunoblot

FIG. 2C

32 P-Poly peptides

FIG. 3B

Immunoblot

FIG. 3C

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3000 -t

Additions:
First PMA(1nM)

none

1 h

24h

24 h

24h

PMA(1nM)
Second —

15m

EGF(50ng/ml)

1 5m

FIG. 2D

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Raf variants: 1 234 56789 10 11 12

WT Raf

Raf<84-87A)

+■

PKCy/Raf

♦

PKC//Raf(84-87A)

Cell treatment:

Minus serum

Plus EGF

♦

Plus TPA

+ i

FIG. 3A

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6/8

40
CO

" <

to °P

CO (0

CC QC

II II

<N CO

s 5

CO
CM

WO 97/34146

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7/8

FIG. 5A

1 2

Raf expression,
COS extract

1 = WT Raf

2 = Raf(84-87A)

3 = PKCtfRaf(84-87A)

4 = PKC-j/Raf

FIG. 5B

Raf retained
by COS Ras[V12]

Raf expression,
COS extract

1 = WT Raf

2 = Raf(C165,168S)

3 = Raf(84-87A)
4=PKCy/Raf

FIG. 6A

Raf retained
p|Q gg b y Bacterial GST-Ras/GTPTS

WO 97/34146

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PCT/US97/03881

FIG. 7 A

Processed Ras
GDP GTP

,,,. v :-..V.VJM?faj'j!«r!^lJ

Unprocessed Ras
GDP GTP

GST-Raf, 50-150
GST-Raf, 130-220

GST

Anti-Ras blots

FIG. 7B

GST-Raf GST-Raf
50-150 130-220

66
45

Coomassie Blue

INTERNATIONAL SEARCH REPORT

International application No.
PCT/US97/03881

A. CLASSIFICATION OF SUBJECT MATTER

IPC(6) :G01N 33/53, 33/574; A01N 37/18; A61K 38/00
US CL :514/2; 435/7.23
According to International Patent Classification (IPC) or to both national classification and IPC

B. FIELDS SEARCHED

Minimum documentation searched (classification system followed by classification symbols)
U.S. : 514/2; 435/7.23

Documentation searched other than minimum documentation to the extent that such documents are included in the fields searched

Electronic data base consulted during the international search (name of data base and, where practicable, search terms used)
APS, DIALOG

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